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The town is situated on the left bank of the Amur River, 80 kilometers (50 mi) from where it flows into the Amur estuary, 977 kilometers (607 mi) north of Khabarovsk and 582 kilometers (362 mi) from the Komsomolsk-on-Amur railway station. It is the closest significant settlement to the Strait of Tartary separating the mainland from Sakhalin.

In the late Middle Ages, the people living along the lower course of the Amur (Nivkh, Oroch, Evenki) were collectively known in China as the "wild Jurchen". The Yuan Dynasty Mongols sent expeditions to this area with an eye toward using the region as a base for attack on Japan, or for defending against the SakhalinAinus. According to the History of Yuan, in 1264 the Nivkhs recognized the Mongol sovereignty. In 1263, the Mongols set up the "Command Post of the Marshal of the Eastern Campaign" near the modern settlement of Tyr, some 100 kilometers (62 mi) upstream from today's Nikolayevsk-on-Amur. At roughly the same time, a shrine was built on the Tyr Rock.[9][10]

From 1411 to 1433, the MingeunuchYishiha, a man of Haixi Jurchen origin, led four large missions to win over the allegiance of the "Jurchen" tribes along the Sunggari and Amur Rivers. During this time, the Yongning Temple was constructed at Tyr, and stelae with inscriptions erected.[9]

The town emerged as an important commercial harbor; however, due to navigational difficulties caused by the sand banks in the Amur estuary and sea ice making the harbor unusable for five months each year, the main center for Russian shipping were transferred to the better situated Vladivostok in the early 1870s. The town remained the administrative center of this region until 1880, when the governor relocated to Khabarovsk. Anton Chekhov, visiting the town on his journey to Sakhalin in 1890, noted its rapid depopulation, although this trend was slowed somewhat in the late 1890s by the discovery of gold and establishment of salmon fisheries.

During the Russian Civil War, the town's population plummeted from 15,000 to 2,000, as a local partisan leader, later executed by the same Bolsheviks he was supposed to be aligned with, razed the entire town to the ground and massacred the minority Japanese population along with most of the Russian population.

Around 1940, a prison camp of the gulag system was located in the town.[12]

Nikolayevsk-on-Amur has a borderline humid continental climate (KöppenDfb), almost cold enough to be a subarctic climate (Dfc). Precipitation is not as low in the winter as over most of Siberia since the coast in on the fringe of influence from the Aleutian Low. The near-maritime location only marginally—by 5 °C (9.0 °F)—moderates the winters compared to interior Siberia, but makes the summers noticeably cool (especially in May and June) though the Oyashio fogs are less prevalent than on Sakhalin itself and sunshine hours therefore rather longer.